def __init__(self,
effects,
distinct=False,
sort_key=None,
sources=set([])):
"""
Parameters
----------
effects : list
Collection of any class which is compatible with the sort key
distinct : bool
Only keep distinct entries or allow duplicates.
sort_key : fn
Function which maps each element to a sorting criterion.
sources : set
Set of files from which this collection was generated.
"""
self.effects = effects
Collection.__init__(self,
elements=effects,
distinct=distinct,
sort_key=sort_key,
sources=sources)
def __init__(
self,
binding_predictions,
path=None,
distinct=True,
sort_key=lambda x: x.value):
Collection.__init__(
self,
elements=binding_predictions,
sources=[path] if path else [],
distinct=distinct,
sort_key=sort_key)
def __init__(
self,
variants,
distinct=True,
sort_key=variant_ascending_position_sort_key,
sources=None,
source_to_metadata_dict={}):
"""
Construct a VariantCollection from a list of Variant records.
Parameters
----------
variants : iterable
Variant objects contained in this VariantCollection
distinct : bool
Don't keep repeated variants
sort_key : callable
sources : set
Optional set of source names, may be larger than those for
which we have metadata dictionaries.
source_to_metadata_dict : dict
Dictionary mapping each source name (e.g. VCF path) to a dictionary
from metadata attributes to values.
"""
self.source_to_metadata_dict = source_to_metadata_dict
self.variants = variants
if sources is None:
sources = set(source_to_metadata_dict.keys())
if any(source not in sources for source in source_to_metadata_dict.keys()):
raise ValueError(
"Mismatch between sources=%s and keys of source_to_metadata_dict=%s" % (
sources,
set(source_to_metadata_dict.keys())))
Collection.__init__(
self,
elements=variants,
distinct=distinct,
sort_key=sort_key,
sources=sources)
def __init__(self,
variants,
distinct=True,
sort_key=variant_ascending_position_sort_key,
sources=None,
source_to_metadata_dict={}):
"""
Construct a VariantCollection from a list of Variant records.
Parameters
----------
variants : iterable
Variant objects contained in this VariantCollection
distinct : bool
Don't keep repeated variants
sort_key : callable
sources : set
Optional set of source names, may be larger than those for
which we have metadata dictionaries.
source_to_metadata_dict : dict
Dictionary mapping each source name (e.g. VCF path) to a dictionary
from metadata attributes to values.
"""
self.source_to_metadata_dict = source_to_metadata_dict
self.variants = variants
if sources is None:
sources = set(source_to_metadata_dict.keys())
if any(source not in sources
for source in source_to_metadata_dict.keys()):
raise ValueError(
"Mismatch between sources=%s and keys of source_to_metadata_dict=%s"
% (sources, set(source_to_metadata_dict.keys())))
Collection.__init__(self,
elements=variants,
distinct=distinct,
sort_key=sort_key,
sources=sources)
def __init__(self, effects, distinct=False, sort_key=None, sources=set([])):
"""
Parameters
----------
effects : list
Collection of any class which is compatible with the sort key
distinct : bool
Only keep distinct entries or allow duplicates.
sort_key : fn
Function which maps each element to a sorting criterion.
sources : set
Set of files from which this collection was generated.
"""
self.effects = effects
Collection.__init__(
self,
elements=effects,
distinct=distinct,
sort_key=sort_key,
sources=sources)
def clone_with_new_elements(self, new_elements):
return Collection.clone_with_new_elements(
self, new_elements, rename_dict={"elements": "effects"})
def clone_with_new_elements(self, new_elements):
return Collection.clone_with_new_elements(
self,
new_elements,
rename_dict={"elements": "effects"})